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- PDB-6tfr: Linalool Dehydratase Isomerase C180A mutant -

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Basic information

Entry
Database: PDB / ID: 6tfr
TitleLinalool Dehydratase Isomerase C180A mutant
ComponentsLinalool dehydratase-isomerase protein LDI
KeywordsLYASE / Alkene / Alkenol / Hydratase
Function / homology
Function and homology information


linalool dehydratase / geraniol isomerase / monoterpene catabolic process / intramolecular hydroxytransferase activity / monoterpenoid metabolic process / hydro-lyase activity / cellular response to organic substance / protein tetramerization / periplasmic space
Similarity search - Function
Linalool dehydratase/isomerase / Linalool dehydratase/isomerase
Similarity search - Domain/homology
Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCastellaniella defragrans 65Phen (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCuetos, A. / Zukic, E. / Danesh-Azari, H.R. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P005578/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms
Authors: Cuetos, A. / Iglesias-Fernandez, J. / Danesh-Azari, H.R. / Zukic, E. / Dowle, A. / Osuna, S. / Grogan, G.
History
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Linalool dehydratase-isomerase protein LDI
B: Linalool dehydratase-isomerase protein LDI
C: Linalool dehydratase-isomerase protein LDI
D: Linalool dehydratase-isomerase protein LDI
E: Linalool dehydratase-isomerase protein LDI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,78415
Polymers210,1645
Non-polymers62110
Water37,4892081
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13690 Å2
ΔGint-28 kcal/mol
Surface area61880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 106.970, 123.670
Angle α, β, γ (deg.)90.000, 95.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: 0 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA3 - 3644 - 365
21GLUGLUBB3 - 3644 - 365
12GLUGLUAA3 - 3644 - 365
22GLUGLUCC3 - 3644 - 365
13GLUGLUAA3 - 3644 - 365
23GLUGLUDD3 - 3644 - 365
14LEULEUAA4 - 3645 - 365
24LEULEUEE4 - 3645 - 365
15ALAALABB2 - 3643 - 365
25ALAALACC2 - 3643 - 365
16GLUGLUBB3 - 3654 - 366
26GLUGLUDD3 - 3654 - 366
17LEULEUBB4 - 3655 - 366
27LEULEUEE4 - 3655 - 366
18GLUGLUCC3 - 3644 - 365
28GLUGLUDD3 - 3644 - 365
19LEULEUCC4 - 3645 - 365
29LEULEUEE4 - 3645 - 365
110LEULEUDD4 - 3655 - 366
210LEULEUEE4 - 3655 - 366

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Linalool dehydratase-isomerase protein LDI


Mass: 42032.734 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: C180A mutant
Source: (gene. exp.) Castellaniella defragrans 65Phen (bacteria)
Gene: BN940_14136 / Production host: Escherichia coli (E. coli) / References: UniProt: W8X534
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2081 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.02 M phosphate; 0.1 M bis-Tris propane pH 6.5; 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.45→55.32 Å / Num. obs: 371363 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.05 / Net I/σ(I): 9.8
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.72 / Num. unique obs: 27532 / CC1/2: 0.55 / Rpim(I) all: 0.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1U

5g1u


Resolution: 1.45→55.32 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.084 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 18367 4.9 %RANDOM
Rwork0.1566 ---
obs0.1576 352946 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.06 Å2 / Biso mean: 18.756 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.21 Å2
2---0.54 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.45→55.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14480 0 40 2097 16617
Biso mean--28.23 32.95 -
Num. residues----1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01315261
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713775
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.64420802
X-RAY DIFFRACTIONr_angle_other_deg1.6091.5731858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51251894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2621.369833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.676152355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.07415106
X-RAY DIFFRACTIONr_chiral_restr0.1080.21906
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217363
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023511
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A123830.08
12B123830.08
21A125060.06
22C125060.06
31A123430.07
32D123430.07
41A123700.07
42E123700.07
51B123950.07
52C123950.07
61B123500.08
62D123500.08
71B124290.07
72E124290.07
81C124030.07
82D124030.07
91C124080.07
92E124080.07
101D124380.07
102E124380.07
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 1313 -
Rwork0.343 26022 -
all-27335 -
obs--99.79 %

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